It is not possible for Nintendo to block Smash Stack with an update because an update changes the System Menu, which is not running when a game (e.g. Brawl) is running. Therefore changes to it would not affect Brawl, and hence not affect Smash Stack. An IOS update probably could do it, but it'd need a LOT of testing to make completely sure that there are NO issues caused by such a big change to an IOS, as a few games at least use IOS36. This is the reason new IOS are added, rather than the old ones updated, so as to ensure 100% compatibility, with no chance of IOS updates breaking older games.
The only way to do it would be if Nintendo adding some sort of Ocarina-style patching to the System Menu, to patch Brawl as it loads, and write a patch to stop Smash Stack working, but I dunno if Nintendo would ever go to that much trouble. Writing an entire patching engine from scratch, for a system they never intended to be able to patch games, would be a large job.